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Lowering barriers to
publishing biological data on
          the web
           Brad Chapman
        Department of Molecul...
Motivation
Motivation

    Web accessible
    Interoperable in standard formats
    Displays for browsing
    Analyses
    Scale
Current state: Reusable libraries
      Parse file formats
      Run programs
      Build analysis pipelines
      Communit...
Current state: Database schemas


     Represent biological data
     Expand analyses beyond flat files
     Interoperate wi...
Current state: Web applications
Faster and Bigger
Proposal
    Provide
           Reusable presentation components
           Quickly deployable frameworks

    Integrate
 ...
Proposal
http://biosqlweb.appspot.com/
Challenges: Design
     Reusable
         Components: avoid large framework
         Multi-language: javascript front end
...
Challenges: Community questions

 How do we. . .
    provide plug-in components?
    leverage existing code?
    make reus...
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Chapman_publishingweb_BOSC2009

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Chapman_publishingweb_BOSC2009

  1. 1. Lowering barriers to publishing biological data on the web Brad Chapman Department of Molecular Biology Massachusetts General Hospital Boston, MA USA chapmanb@50mail.com http://friendfeed.com/chapmanb 27 June 2009
  2. 2. Motivation
  3. 3. Motivation Web accessible Interoperable in standard formats Displays for browsing Analyses Scale
  4. 4. Current state: Reusable libraries Parse file formats Run programs Build analysis pipelines Communities Python examples Biopython pygr bx-python PyCogent
  5. 5. Current state: Database schemas Represent biological data Expand analyses beyond flat files Interoperate with standards BioSQL Chado
  6. 6. Current state: Web applications
  7. 7. Faster and Bigger
  8. 8. Proposal Provide Reusable presentation components Quickly deployable frameworks Integrate Bioinformatics libraries Database schemas Web development frameworks
  9. 9. Proposal
  10. 10. http://biosqlweb.appspot.com/
  11. 11. Challenges: Design Reusable Components: avoid large framework Multi-language: javascript front end Accessible Automated data retrieval (REST) Standard formats (GFF, RDF) Available Creative Commons http://creativecommons.org/about/licenses Open Data Commons http://www.opendatacommons.org/licenses/
  12. 12. Challenges: Community questions How do we. . . provide plug-in components? leverage existing code? make reuse easier? communicate about these issues?

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